Scripts here are to help with creating input for the nextflow pipeline, they are not directly run during the workflow.
symlink_exeter.py
Input FASTQ files are expected to be in the folder structure {lab}/{run_id}/{sample_id}*.fastq.gz but samples from exeter are not in this format.
To get around this constraint, symlinks to the input are created using symlink_exeter.py script.
This should be run with the ww_minimal conda activated.
python3 symlink_exeter.py <INPUT SAMPLE CSV> <FASTQ SOURCE DIRECTORY> <DESTINATION DIRECTORY>